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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcaacaattctaaagggtagatcatatctgctgcccgacatcactgatatttgataaattatatttctatagccaaaagcttatttaagttttgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAGTATTCGCCAAATTTGAGATGCACCGCC

Basic information

species Vitis vinifera
transcript Vv15s0048g02010.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 10
gtttgtcaacaattctaaagggtagatcatatctgctgcccgacatcactgatatttgataaattatatttctatagccaaaagcttatttaagttttgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAGTATTCGCCAAATTTGAGATGCACCGCC
                     || | |   ||||      | | | ||||    ||  | |  | || |  |  |  |  |||  || |  ||         | ||||||||   |||||| ||||| || |||||||| |||||||| |||||| |||| ||||| |||||||||||| | ||||| || 
---------------------gttggtgg-atctctaattccatagcactttagttctacac-tgatgtaaccttctcacaaaatttttccaa--------ctgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 10
gtttgtcaacaattctaaagggtagatcatatctgct---gcccgacatcactgatatttgataaattatatttctatagccaaaagcttatttaagttttgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAGTATTCGCCAAATTTGAGATGCACCGCC
    || | || ||||      | | |  || |||||   |    | ||     ||| |  |||||| |||  |   |      |  | |   | |    ||  |||||| |||| || ||| ||||||| || |||||||||||||||||||||||||||||||| ||||| |||||| |  | ||||| || 
----gttagcagttctttcctct-gctgctacctgctaaagtattatatgtaatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCT

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 10
gtttgtcaacaattctaaagggtagatcatatctgctgcccgacatcactg-atatttgataaattatatttctatagccaaaagcttatttaagttttgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAGTATTCGCCAAATTTGAGATGCACCGCC
    || | || ||||      | | |  ||||||||     |    |    ||| |  |||||| |||  |   |      |  | |   | |    ||  |||||| |||| || ||| ||||||| || ||||| ||||||||||| ||||||||||| || ||||| |||||| |  | |||||||| 
----gttagcagttctttcttct-gctgctatctgctaaagtattatataatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTGCTGCAATATTCACCAAATCTACGTTGCACCGCT

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G45960.1 (Glycine max), 3'ss of exon 10
gtttgtcaacaattctaaagggtagatcatatctgctgcccgacatcactgatatttgataaattatatttctatagccaaaagcttatttaagttttgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAGTATTCGCCAAATTTGAGATGCACCGCC-
     | | || || |      ||   |  || |||| || |   |     || | | ||  || | ||   |  || || |    |  |  | | || | |  ||| |||| || |||   |||||  ||||||| |||||||| || |||||| ||||||||||||| |||||| |  ||||||| ||  
-----ttagcatttttt-----tactcctcatttgct-cctggagtatgcaatttgtaattgataa-atacttccagtcagagatctgatcgattatt-tatatcaggTTTTTCACAAGAAGATGCCTTCAGAAGCAGTGGATCTAGTGTCAAGGATGCTTCAGTATTCACCAAATCTACGATGCACTGCTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|349820373|gb|FQ403989.1|FQ403989
EST:     ATTACAATGAGTTCAAGTTTCCACAAATCAAAGCTCACCCATGGCACAAG                         CTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTG
genomic: ATTACAATGAGTTCAAGTTTCCACAAATCAAAGCTCACCCATGGCACAAGgtttgtcaac ... tgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTG
EST: gi|110688693|gb|EE067533.1|EE067533
EST:     ATTACAATGAGTTCAAGTTTCCACAAATCAAAGCTCACCCATGGCACAAG                         CTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCANGGCTG
genomic: ATTACAATGAGTTCAAGTTTCCACAAATCAAAGCTCACCCATGGCACAAGgtttgtcaac ... tgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTG
EST: gi|32249937|gb|CD715756.1|CD715756
EST:     TACA-TGAGTTTCA-GTTTCCACAAATNCAA-GCTCACCCATGGCACAAG                         CTTTTCCATAAGCGAATGCCCCCA
genomic: TACAATGAGTT-CAAGTTTCCACAAAT-CAAAGCTCACCCATGGCACAAGgtttgtcaac ... tgttttccagCTTTTCCATAAGCGAATGCCCCCA
EST: gi|30328496|gb|CD011758.1|CD011758
EST:     TTCCACAAATCAAAGCTCACCCATGGCACAAG                         CTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTG
genomic: TTCCACAAATCAAAGCTCACCCATGGCACAAGgtttgtcaac ... tgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTG
EST: gi|22009072|gb|BQ794106.1|BQ794106
EST:     CCATGGCACAAG                         CTTTTCCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCT
genomic: CCATGGCACAAGgtttgtcaac ... tgttttccagCTTTT-CCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCT
EST: gi|110732276|gb|EE107431.1|EE107431
EST:     ATTACAATGAGTTCAAGTTTCCACAAATCAAAGCTCACCCATGGCACAAG                         CTTTTCCATAAGCGAATGCCCCCANAAGCTGTGGATCTTGTATCAAGGCTG
genomic: ATTACAATGAGTTCAAGTTTCCACAAATCAAAGCTCACCCATGGCACAAGgtttgtcaac ... tgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTG
EST: gi|37189535|gb|CF608884.1|CF608884
EST:     ATTACAATGAGTTCAAGTTTCCACAAATCAAAGCTCACCCATGGCACAAG                         CTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTG
genomic: ATTACAATGAGTTCAAGTTTCCACAAATCAAAGCTCACCCATGGCACAAGgtttgtcaac ... tgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgataaattatatttctatagccaaaagcttatttaagttttgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAGTATTCGCCAAATTTGAGATGCACCGCC
 atttgat  putative branch site (score: 5)
                                          ttttgttttcc  putative PPT
      ataaattatatttcta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtcaacaattctaaagggtagatcatatctgctgcccgacatcactgatatttgataaattatatttctatagccaaaagcttatttaagttttgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAGTATTCGCCAAATTTGAGATGCACCGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG